PDB-4wit: TMEM16 lipid scramblase in crystal form 2

ID or keywords:

Entry

Database: PDB / ID: 4wit

Title

TMEM16 lipid scramblase in crystal form 2

Components

Predicted protein

Protein structure prediction

Keywords

LIPID TRANSPORT /

membrane protein / calcium activation /

transport protein

Function / homology

: / Alpha-beta plait domain in TMEM16 lipid scramblase /

Anoctamin /

: /

Calcium-activated chloride channel /

membrane / identical protein binding /

metal ion binding / Plasma membrane channel protein

Function and homology information

Biological species

Nectria haematococca (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.4 Å

Authors

Dutzler, R. / Brunner, J.D. / Lim, N.K. / Schenck, S.

Funding support

Switzerland, 2items

Citation

Journal: Nature / Year: 2014
Title: X-ray structure of a calcium-activated TMEM16 lipid scramblase.
Authors: Brunner, J.D. / Lim, N.K. / Schenck, S. / Duerst, A. / Dutzler, R.

History

Deposition	Sep 26, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Nov 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 19, 2014	Group: Database references
Revision 1.2	Dec 17, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wit.cif.gz	545.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4wit.ent.gz	470.1 KB	Display	PDB format
PDBx/mmJSON format	4wit.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wi/4wit ftp://data.pdbj.org/pub/pdb/validation_reports/wi/4wit	HTTPS FTP

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Related structure data

Related structure data	4wisC C: citing same article (ref.)
Similar structure data	4wis-d 6qm9-d 6qma-d 6qm5-d 6qm4-d 6qmb-d 6qm6-d 2ch5-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Predicted protein

B: Predicted protein

hetero molecules

167 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	115.940, 127.240, 180.110
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Predicted protein / Protein structure prediction Mass: 83200.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nectria haematococca (fungus) / Strain: 77-13-4 / ATCC MYA-4622 / FGSC 9596 / MPVI / Gene: NECHADRAFT_66456 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: C7Z7K1
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

#1: Protein

Predicted protein /

Protein structure prediction

Mass: 83200.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Nectria haematococca (fungus) / Strain: 77-13-4 / ATCC MYA-4622 / FGSC 9596 / MPVI / Gene: NECHADRAFT_66456 / Production host:

Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: C7Z7K1

#2: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.99 Å³/Da / Density % sol: 69.19 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 21-23% PEG400, 50 mM HEPES pH 7.4, 100 mM Ammonium sulfate PH range: 7.4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 10, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.4→50 Å / Num. obs: 36952 / % possible obs: 98.9 % / Redundancy: 9.6 % / R_merge(I) obs: 0.065 / Net I/σ(I): 20
Reflection shell	Resolution: 3.4→3.5 Å / Redundancy: 8.6 % / R_merge(I) obs: 1.47 / Mean I/σ(I) obs: 1.7 / % possible all: 87.9

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_1760)	refinement
XDS		data reduction
SHELX		phasing
SHARP		phasing
DM		phasing
O		model building
Coot		model building
SCALEPACK		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 3.4→14.997 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2917	1596	4.38 %
R_work	0.2477	-	-
obs	0.2498	36451	98.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.4→14.997 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10570	0	4	0	10574

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	10846
X-RAY DIFFRACTION	f_angle_d	0.699	14716
X-RAY DIFFRACTION	f_dihedral_angle_d	15.16	3892
X-RAY DIFFRACTION	f_chiral_restr	0.026	1618
X-RAY DIFFRACTION	f_plane_restr	0.003	1864

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.4001-3.5085	0.3292	61	0.3267	2880	X-RAY DIFFRACTION	89
3.5085-3.6322	0.3529	94	0.3092	3216	X-RAY DIFFRACTION	100
3.6322-3.7754	0.3801	132	0.3044	3164	X-RAY DIFFRACTION	100
3.7754-3.9443	0.3791	157	0.2901	3141	X-RAY DIFFRACTION	100
3.9443-4.148	0.3571	152	0.2756	3166	X-RAY DIFFRACTION	100
4.148-4.4017	0.3101	145	0.2538	3180	X-RAY DIFFRACTION	100
4.4017-4.7317	0.2832	160	0.2258	3181	X-RAY DIFFRACTION	100
4.7317-5.1898	0.2734	181	0.2211	3167	X-RAY DIFFRACTION	100
5.1898-5.9004	0.3033	166	0.2481	3201	X-RAY DIFFRACTION	100
5.9004-7.289	0.3362	162	0.276	3247	X-RAY DIFFRACTION	100
7.289-14.997	0.2399	186	0.2156	3312	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.6861	1.8099	-0.6515	6.3586	0.1607	5.0438	-1.0795	0.3741	0.0693	-1.2728	0.6084	0.2839	0.389	-0.4192	0.3153	1.5885	-0.2389	0.0755	1.5505	-0.1514	1.121	18.7927	14.634	-27.0853
2	4.8311	0.1986	1.2927	2.8014	-0.0941	5.7452	-0.6819	1.4958	-0.9678	-0.756	0.7135	-0.7907	0.0585	1.0802	-0.1039	0.8977	-0.0492	0.3218	0.8639	-0.0592	1.221	32.6226	11.2085	-11.1362
3	4.0508	0.7184	0.5163	3.0034	-0.2806	3.1326	-0.0381	0.0607	-0.4822	-0.2698	0.063	-0.2495	0.4154	-0.4104	0.0126	0.5902	0.002	0.0264	0.5793	0.0205	0.7481	18.8323	8.7184	7.8253
4	2.1557	0.6853	-0.6141	3.6767	-1.4688	4.9097	-0.1556	-0.009	-0.7726	-0.4227	-0.0225	-0.8481	1.5848	-0.1256	0.0615	1.0272	0.0552	0.1091	0.6522	-0.0588	1.2712	27.2992	-4.8086	6.1159
5	1.1979	0.9359	-0.1254	3.796	-0.0281	1.033	-0.1012	-0.075	0.2885	-0.1769	0.1183	-0.1375	-0.3975	-0.1662	-0.0615	0.8596	0.1077	-0.069	0.9817	0.0725	1.2	34.1955	46.987	9.3132
6	2.3322	1.4509	-0.0992	4.4093	-1.8738	2.0283	-0.2003	0.0989	1.1869	0.2796	0.3141	0.6551	-0.6744	-0.3904	-0.3956	0.8255	0.1573	-0.0618	0.7631	-0.0065	1.2835	24.6742	58.4646	13.2193
7	2.0915	-0.0237	-0.5943	3.0249	0.1069	3.1103	0.1901	-0.4909	0.2747	0.6499	-0.2214	-0.0918	-0.5925	-0.0539	-0.222	0.798	-0.0432	-0.0344	0.8455	-0.0461	0.8676	29.5377	46.8379	34.1136
8	0.2785	0.0878	0.3022	2.2824	1.5298	3.8036	-0.1268	0.1589	-0.0603	-0.6839	-0.1001	-0.0644	0.5235	-0.4036	0.189	1.094	-0.1844	0.0855	1.2367	0.1318	1.1337	19.0055	22.5713	-6.0224

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 103 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 104 through 211 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 212 through 391 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 392 through 558 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 559 through 719 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 19 through 245 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 246 through 558 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 559 through 719 )

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